Chapter 4: 4.4 Characteristics of Membrane Proteins

Question 1

What are the two types of proteins in the lipid bilayer?

Answer 1

• Peripheral
• Integral

Question 2

Define:

Glycoproteins

Answer 2

Proteins with lipid post-translational modifications that aid in membrane insertion and cell recognition

Question 3

What are the two types of integral proteins?

Answer 3

1. Transmembrane
2. Monotopic

Question 4

List:

Ways peripheral membrane proteins can be attached to the membrane

Answer 4

1. Amphipathic helices
2. Hydrophobic loop regions
3. Attachment to integral proteins
4. Ionic and H-bonds

Question 5

What are the methods to remove peripheral membrane proteins?

Answer 5

1. High salt method
2. pH change

Question 6

Describe:

Removal of Peripheral Membrane Proteins via High salt method

Answer 6

• Neutralizes or “shields” charges using ions in salt
• Breaks hydrogen bonds and ionic interactions

Question 7

Describes:

Removal of Peripheral Membrane Proteins via pH change

Answer 7

• Protonates/deprotonates charged amino acids
• Breaks hydrogen bonds and ionic interactions

Question 8

Define:

Integral Membrane Proteins

Answer 8

Completely span the membrane

Question 9

How many types of integral membrane proteins are there?

Answer 9

6

Question 10

Describe:

Each type of integral membrane proteins

Answer 10

1. Type I: Single pass amino group (NH3+) on outside
2. Type II: Single pass amino group (NH3+) on inside
3. Type III: Single protein with multiple passes
4. Type IV: Multiple proteins each with single passes
5. Type V: Held to membrane via lipid anchor
6. Type VI: Held to membrane via trans-membrane segment and lipid anchor

Question 11

What are the regions of the cellular membrane?

Answer 11

1. Extracellular-facing region
2. Membrane spanning regions
3. Intracellular-facing region

Question 12

State:

Purpose of Extracellular-facing region

Answer 12

Play roles in signalling, transport, and cell recognition and communication (Lipids and glycosylated proteins)

Question 13

State:

Purpose of Membrane spanning regions

Answer 13

~20 amino acids long and mostly hydrophobic

Question 14

State:

Purpose of Intracellular-facing region

Answer 14

Transmit signals to the cytosol through “tails” and are involved in transport

Question 15

How are integral membrane proteins removed?

Answer 15

Requires harsh removal (detergents or organic solvents)
* Detergents separate proteins from lipids

Question 16

How is amino acid hydrophobicity measured?

Answer 16

1. Partitioning method
2. Surface exposure

Question 17

In the partitioning method:

How is amino acid hydrophobicity measured?

Answer 17

Observe amino acid distribution between organic solvent (non-polar) and aqueous solvents (polar)

Question 18

In the partitioning method:

What are two solvents used to mimic conditions for the partitioning methods?

Answer 18

1. n-octanol (non-polar): Close to conditions of membrane interior
2. Water (polar): Close to conditions of cytosol

Question 19

State:

The formula for partition coefficient

Answer 19

P(AA) = C(AA nonpolar) / C(AA polar)

Question 20

True or False:

The partition coefficient is reported as the formula

Answer 20

Not exactly, often reported as log of this value

Question 21

Are polar or non-polar amino acids found on the surface of proteins?

Answer 21

Polar

Question 22

Are polar or non-polar amino acids found in the interior of proteins?

Answer 22

Non-polar

Question 23

The average accessibility of each amino acid is determined by…

Answer 23

From the coordinates of 12 model globular proteins

Question 24

What is hyrdropathy calculated as in surface exposure?

Answer 24

As the fraction of the total number of the protein that is at least 95% buried from the surface

Question 25

Describe:

The process of Assigning Transmembrane Sequences based on Hydropathy

Answer 25

1. Assign hydropathy value to each residue in the protein (either a positive or negative value) - using Kyte-Doolittle Hydropathy scale
2. In a series of 7 residues the average of the seven values is assigned to amino acid in position 4
3. Move over one residue and perform calculation
4. Plot on grid

Question 26

What is a problem when trying to span the non-polar membrane?

Answer 26

The polar backbone

Question 27

How is a non-polar membrane spanned?

Answer 27

Typically form alpha-helix 20-25 amino acids long to span 3-4 nm membrane

Question 28

True or False:

100% of single spanning proteins utilize the alpha-helix

Answer 28

True

Question 29

Besides the polar backbond in a non-polar membrane, what is another issue in membrane protein folding?

Answer 29

The fact that most hydrophobic residues have a higher propernsity to form beta-sheets

Question 30

Hydrophobic resides having a higher propensity to form beta sheets is based on…

Answer 30

Chou-Fasman parameters

Question 31

Due to hydrophobic residues:

The need to neutralize ——– and ————– are a higher priority and supersede these ———-

Answer 31

1. Backbone
2. Hydrophobicity
3. Parameters

Question 32

What do most transmembrane proteins contain? Why?

Answer 32

Often contain Gly
* For helix-helix interactions
* As most transmembrane proteins span the membrane multiple times